Previous studies have demonstrated that infrared (IR) intraoperative imaging is a reliable tool to identify perfusion of brain tumors and kidneys in human surgery. To explore further imaging specific to organ structure and ischemic injuries, intraoperative IR imagery was performed on porcine and rat models. Ureter (poricine model): IR imaging enabled a surgeon to view, record, replay, print, and archive high quality, real-time images of a ureter during infusion of room temperature solution as a contrast agent. IR imaging was repeated multiple times by slightly changing the temperature of an infused saline (cooler or warmer then previous bolus by 1 degree C). Synthesis of derivative images from collected IR images allowed visualization of the velocity pattern of the bolus within the ureter and, therefore, any non-uniformity of structures within the ureter. Fusion of IR and visible images allowed outlining the ureter based on functional (IR) and surface structural features. Kidney (porcine and rat models): The IR method allowed visualization of gross renal perfusion. IR imaging immediately showed what segment of the kidney was occluded or reperfused. Further analysis of the IR data demonstrated that low frequency oscillations attenuated substantially at the site of ischemic segments, but not in the perfused segments of the kidney. Intraoperative imaging offers a promising modality for real-time ureteral identification and assessment of renal perfusion. Kidney perfusion focal deficits were easily identified using IR imaging, even without bolus injection. Observed low frequency blood flow oscillations were possibly related to local vasomotion and endothelial layer damage at the site of ischemia. This phenomenon may be useful for the assessment of ischemic injury and endothelial cell integrity.